LLC received Security Deposit

The partnership, owned by my spouse and myself only (we file personal taxes Jointly) received the 2024 1099-MISC from our one and only tenant. This year, the lease was extended for another 5 years and the tenant paid us an additional amount (for conversation let's say $3,000) to their security deposit. Our books show the original security deposit as a liability. As a result, when I received the $3,000, I booked the additional security deposit amount as a liability.  Here's my problem...The $3,000 is included in the amount of the1099-MISC.  I'm wondering what I'm supposed to do with Quickbooks entry or if TT will ask a question later that will fix this discrepancy. I appreciate the assistance.